diff --git a/Figure Handlers/PowerSpectrumFigureHandler.m b/Figure Handlers/PowerSpectrumFigureHandler.m
new file mode 100644
index 0000000..4e0d516
--- /dev/null
+++ b/Figure Handlers/PowerSpectrumFigureHandler.m	
@@ -0,0 +1,124 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+classdef PowerSpectrumFigureHandler < FigureHandler
+    
+    properties (Constant)
+        figureType = 'Power Spectrum'
+    end
+    
+    properties
+        meanPlots   % array of structures to store the properties of each class of epoch.
+        meanParamNames
+    end
+    
+    methods
+        
+        function obj = PowerSpectrumFigureHandler(protocolPlugin, varargin)
+            obj = obj@FigureHandler(protocolPlugin); 
+            
+            xlabel(obj.axesHandle(), 'sec');
+            set(obj.axesHandle(), 'XTickMode', 'auto');
+            
+            obj.resetPlots();
+            
+            ip = inputParser;
+            ip.addParamValue('GroupByParams', {}, @(x)iscell(x) || ischar(x));
+            ip.parse(varargin{:});
+            
+            if iscell(ip.Results.GroupByParams)
+                obj.meanParamNames = ip.Results.GroupByParams;
+            else
+                obj.meanParamNames = {ip.Results.GroupByParams};
+            end
+        end
+        
+        
+        function handleCurrentEpoch(obj)
+            [responseData, sampleRate, units] = obj.protocolPlugin.response();
+            responseData = fft(responseData);
+            responseData = responseData.*conj(responseData);
+
+            % Get the parameters for this "class" of epoch.
+            % An epoch class is defined by a set of parameter values.
+            if isempty(obj.meanParamNames)
+                % Automatically detect the set of parameters.
+                epochParams = obj.protocolPlugin.epochSpecificParameters();
+            else
+                % The protocol has specified which parameters to use.
+                for i = 1:length(obj.meanParamNames)
+                    epochParams.(obj.meanParamNames{i}) = obj.protocolPlugin.epoch.ProtocolParameters.Item(obj.meanParamNames{i});
+                end
+            end
+            
+            % Check if we have existing data for this class of epoch.
+            meanPlot = struct([]);
+            for i = 1:numel(obj.meanPlots)
+                if isequal(obj.meanPlots(i).params, epochParams)
+                    meanPlot = obj.meanPlots(i);
+                    break;
+                end
+            end
+            
+            if isempty(meanPlot)
+                % This is the first epoch of this class to be plotted.
+                meanPlot = {};
+                meanPlot.params = epochParams;
+                meanPlot.data = responseData;
+                meanPlot.sampleRate = sampleRate;
+                meanPlot.units = [units,'^2'];
+                meanPlot.count = 1;
+                hold(obj.axesHandle(), 'on');
+                meanPlot.plotHandle = loglog(obj.axesHandle(), (1:length(meanPlot.data)/2) * sampleRate, meanPlot.data(1:length(meanPlot.data)/2));
+                obj.meanPlots(end + 1) = meanPlot;
+            else
+                % This class of epoch has been seen before, add the current response to the mean.
+                % TODO: Adjust response data to the same sample rate and unit as previous epochs if needed.
+                % TODO: if the length of data is varying then the mean will not be correct beyond the min length.
+                meanPlot.data = (meanPlot.data * meanPlot.count + responseData) / (meanPlot.count + 1);
+                meanPlot.count = meanPlot.count + 1;
+                set(meanPlot.plotHandle, 'XData', (1:length(meanPlot.data)/2) * sampleRate, ...
+                                         'YData', meanPlot.data);
+                obj.meanPlots(i) = meanPlot;
+            end
+            
+            % Update the y axis with the units of the response.
+            ylabel(obj.axesHandle(), [units,'^2']);
+            
+            if isempty(epochParams)
+                titleString = 'All epochs grouped together.';
+            else
+                paramNames = fieldnames(epochParams);
+                titleString = ['Grouped by ' humanReadableParameterName(paramNames{1})];
+                for i = 2:length(paramNames) - 1
+                    titleString = [titleString ', ' humanReadableParameterName(paramNames{i})];
+                end
+                if length(paramNames) > 1
+                    titleString = [titleString ' and ' humanReadableParameterName(paramNames{end})];
+                end
+            end
+            title(obj.axesHandle(), titleString);
+        end
+        
+        
+        function clearFigure(obj)
+            obj.resetPlots();
+            
+            clearFigure@FigureHandler(obj);
+        end
+        
+        
+        function resetPlots(obj)
+            obj.meanPlots = struct('params', {}, ...        % The params that define this class of epochs.
+                                   'data', {}, ...          % The mean of all responses of this class.
+                                   'sampleRate', {}, ...    % The sampling rate of the mean response.
+                                   'units', {}, ...         % The units of the mean response.
+                                   'count', {}, ...         % The number of responses used to calculate the mean reponse.
+                                   'plotHandle', {});       % The handle of the plot for the mean response of this class.
+        end
+        
+    end
+    
+end
\ No newline at end of file
diff --git a/Protocols/Grid/allcombs.m b/Protocols/Grid/allcombs.m
deleted file mode 100644
index 71ef394..0000000
--- a/Protocols/Grid/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/HotspotsDS/allcombs.m b/Protocols/HotspotsDS/allcombs.m
deleted file mode 100755
index 71ef394..0000000
--- a/Protocols/HotspotsDS/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/LEDFlash/LEDFlash.m b/Protocols/LEDFlash/LEDFlash.m
new file mode 100644
index 0000000..68cef69
--- /dev/null
+++ b/Protocols/LEDFlash/LEDFlash.m
@@ -0,0 +1,134 @@
+% Creates a single stimulus composed of mean + flash.
+% Implements SymphonyProtocol
+%
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+%
+%  Modified by TA 9.8.12 from LED Family to create a single LED pulse protocol
+
+classdef LEDFlash < SymphonyProtocol
+
+    properties (Constant)
+        identifier = 'helsinki.yliopisto.pal'
+        version = 1
+        displayName = 'LED Flash'
+    end
+    
+    properties
+        stimPoints = uint16(100);
+        prePoints = uint16(1000);
+        tailPoints = uint16(4000);
+        stimAmplitude = 0.5;
+        lightMean = 0.0;
+        preSynapticHold = -60;
+        numberOfAverages = uint8(5);
+        interpulseInterval = 0.6;
+        continuousRun = false;
+    end
+    
+    properties (Dependent = true, SetAccess = private) % these properties are inherited - i.e., not modifiable
+        % ampOfLastStep;
+    end
+    
+    methods
+        
+        function [stimulus, lightAmplitude] = stimulusForEpoch(obj, ~) % epoch Num is usually required
+            % Calculate the light amplitude for this epoch.
+            % phase = single(mod(epochNum - 1, obj.stepsInFamily));               % Frank's clever way to determine which flash in a family to deliver
+            lightAmplitude = obj.stimAmplitude; % * obj.ampStepScale ^ phase;   % Frank's clever way to determine the amplitude of the flash family to deliver
+            
+            % Create the stimulus
+            stimulus = ones(1, obj.prePoints + obj.stimPoints + obj.tailPoints) * obj.lightMean;
+            stimulus(obj.prePoints + 1:obj.prePoints + obj.stimPoints) = lightAmplitude;
+        end
+        
+        
+        function stimulus = sampleStimuli(obj) % Return a cell array
+            % you can only create one stimulus with this protocol TA
+            stimulus{1} = obj.stimulusForEpoch();
+        end
+        
+        
+        function prepareRig(obj)
+            % Call the base class method to set the DAQ sample rate.
+            prepareRig@SymphonyProtocol(obj);
+            
+            %obj.setDeviceBackground('LED', obj.lightMean, 'V');
+            
+%             if strcmp(obj.rigConfig.multiClampMode('Amplifier_Ch1'), 'IClamp')
+%                 obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-12, 'A');
+%             else
+%                 obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-3, 'V');
+%             end
+        end
+        
+        
+        function prepareRun(obj)
+            % Call the base class method which clears all figures.
+            prepareRun@SymphonyProtocol(obj);
+
+            obj.openFigure('Response');
+            obj.openFigure('Mean Response', 'GroupByParams', {'lightAmplitude'});
+            obj.openFigure('Response Statistics', 'StatsCallback', @responseStatistics);
+        end
+        
+        
+        function prepareEpoch(obj)
+            % Call the base class method which sets up default backgrounds and records responses.
+            prepareEpoch@SymphonyProtocol(obj);
+            
+            [stimulus, lightAmplitude] = obj.stimulusForEpoch(obj.epochNum);
+            obj.addParameter('lightAmplitude', lightAmplitude);
+            %obj.addStimulus('LED', 'test-stimulus', stimulus, 'V');    %
+            obj.setDeviceBackground('LED', obj.lightMean, 'V');
+            if strcmp(obj.multiClampMode, 'VClamp')
+                obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-3, 'V');
+            else
+                obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-12, 'A');
+            end 
+            obj.addStimulus('LED', 'LED stimulus', stimulus, 'V');    %
+        end
+        
+        
+        function stats = responseStatistics(obj)
+            r = obj.response();
+            
+            % baseline mean and var
+            if ~isempty(r)
+                stats.mean = mean(r(1:obj.prePoints));
+                stats.var = var(r(1:obj.prePoints));
+            else
+                stats.mean = 0;
+                stats.var = 0;
+            end
+        end
+        
+        
+        function completeEpoch(obj)
+            % Call the base class method which updates the figures.
+            completeEpoch@SymphonyProtocol(obj);
+            
+            % Pause for the inter-pulse interval.
+            pause on
+            pause(obj.interpulseInterval);
+        end
+        
+        
+        function keepGoing = continueRun(obj)   
+            % First check the base class method to make sure the user hasn't paused or stopped the protocol.
+            keepGoing = continueRun@SymphonyProtocol(obj);
+            
+            if keepGoing
+                keepGoing = obj.epochNum < obj.numberOfAverages;
+            end
+        end
+        
+        
+%         function amp = get.ampOfLastStep(obj)   % The product of the number of steps in family, the first step amplitude, and the 'scale factor'
+%             amp = obj.baseLightAmplitude * obj.ampStepScale ^ (obj.stepsInFamily - 1);
+%         end
+
+    end
+end
\ No newline at end of file
diff --git a/Protocols/LEDMultiFlash/LEDMultiFlash.m b/Protocols/LEDMultiFlash/LEDMultiFlash.m
new file mode 100644
index 0000000..b390884
--- /dev/null
+++ b/Protocols/LEDMultiFlash/LEDMultiFlash.m
@@ -0,0 +1,134 @@
+% Creates a single stimulus composed of mean + flash for multiple LEDs
+% Implements SymphonyProtocol
+%
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+%
+%  Modified by TA 9.8.12 from LED Family to create a single LED pulse protocol
+classdef LEDMultiFlash < SymphonyProtocol
+
+    properties (Constant)
+        identifier = 'helsinki.yliopisto.pal'
+        version = 1
+        displayName = 'Multi LED Flash'
+    end
+    
+    properties
+        stimPoints = uint16(100);
+        prePoints = uint16(1000);
+        tailPoints = uint16(4000);
+        stimAmplitude = 0.5;
+        lightMean = 0.0;
+        preSynapticHold = -60;
+        numberOfAverages = uint8(5);
+        interpulseInterval = 0.6;
+        continuousRun = false;
+        LED = {'Red_LED','Green_LED','Blue_LED'};
+    end
+    
+    properties (Dependent = true, SetAccess = private) % these properties are inherited - i.e., not modifiable
+        % ampOfLastStep;
+    end
+    
+    methods
+        
+        function [stimulus, lightAmplitude] = stimulusForEpoch(obj, ~) % epoch Num is usually required
+            % Calculate the light amplitude for this epoch.
+            % phase = single(mod(epochNum - 1, obj.stepsInFamily));               % Frank's clever way to determine which flash in a family to deliver
+            lightAmplitude = obj.stimAmplitude; % * obj.ampStepScale ^ phase;   % Frank's clever way to determine the amplitude of the flash family to deliver
+            
+            % Create the stimulus
+            stimulus = ones(1, obj.prePoints + obj.stimPoints + obj.tailPoints) * obj.lightMean;
+            stimulus(obj.prePoints + 1:obj.prePoints + obj.stimPoints) = lightAmplitude;
+        end
+        
+        
+        function stimulus = sampleStimuli(obj) % Return a cell array
+            % you can only create one stimulus with this protocol TA
+            stimulus{1} = obj.stimulusForEpoch();
+        end
+        
+        
+        function prepareRig(obj)
+            % Call the base class method to set the DAQ sample rate.
+            prepareRig@SymphonyProtocol(obj);
+            
+            %obj.setDeviceBackground('LED', obj.lightMean, 'V');
+            
+%             if strcmp(obj.rigConfig.multiClampMode('Amplifier_Ch1'), 'IClamp')
+%                 obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-12, 'A');
+%             else
+%                 obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-3, 'V');
+%             end
+        end
+        
+        
+        function prepareRun(obj)
+            % Call the base class method which clears all figures.
+            prepareRun@SymphonyProtocol(obj);
+
+            obj.openFigure('Response');
+            obj.openFigure('Mean Response', 'GroupByParams', {'lightAmplitude'});
+            obj.openFigure('Response Statistics', 'StatsCallback', @responseStatistics);
+        end
+        
+        
+        function prepareEpoch(obj)
+            % Call the base class method which sets up default backgrounds and records responses.
+            prepareEpoch@SymphonyProtocol(obj);
+            
+            [stimulus, lightAmplitude] = obj.stimulusForEpoch(obj.epochNum);
+            obj.addParameter('lightAmplitude', lightAmplitude);
+            %obj.addStimulus('LED', 'test-stimulus', stimulus, 'V');    %
+            obj.setDeviceBackground(obj.LED, obj.lightMean, 'V');
+            if strcmp(obj.multiClampMode, 'VClamp')
+                obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-3, 'V');
+            else
+                obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-12, 'A');
+            end 
+            obj.addStimulus(obj.LED, sprintf('%s stimulus',obj.LED), stimulus, 'V');    %
+        end
+        
+        
+        function stats = responseStatistics(obj)
+            r = obj.response();
+            
+            % baseline mean and var
+            if ~isempty(r)
+                stats.mean = mean(r(1:obj.prePoints));
+                stats.var = var(r(1:obj.prePoints));
+            else
+                stats.mean = 0;
+                stats.var = 0;
+            end
+        end
+        
+        
+        function completeEpoch(obj)
+            % Call the base class method which updates the figures.
+            completeEpoch@SymphonyProtocol(obj);
+            
+            % Pause for the inter-pulse interval.
+            pause on
+            pause(obj.interpulseInterval);
+        end
+        
+        
+        function keepGoing = continueRun(obj)   
+            % First check the base class method to make sure the user hasn't paused or stopped the protocol.
+            keepGoing = continueRun@SymphonyProtocol(obj);
+            
+            if keepGoing
+                keepGoing = obj.epochNum < obj.numberOfAverages;
+            end
+        end
+        
+        
+%         function amp = get.ampOfLastStep(obj)   % The product of the number of steps in family, the first step amplitude, and the 'scale factor'
+%             amp = obj.baseLightAmplitude * obj.ampStepScale ^ (obj.stepsInFamily - 1);
+%         end
+
+    end
+end
\ No newline at end of file
diff --git a/Protocols/LoomingObjects/allcombs.m b/Protocols/LoomingObjects/allcombs.m
deleted file mode 100644
index 71ef394..0000000
--- a/Protocols/LoomingObjects/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/MovingBar/allcombs.m b/Protocols/MovingBar/allcombs.m
deleted file mode 100644
index 71ef394..0000000
--- a/Protocols/MovingBar/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/MovingGrid/allcombs.m b/Protocols/MovingGrid/allcombs.m
deleted file mode 100644
index 71ef394..0000000
--- a/Protocols/MovingGrid/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/MovingObjects/allcombs.m b/Protocols/MovingObjects/allcombs.m
deleted file mode 100644
index 71ef394..0000000
--- a/Protocols/MovingObjects/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/PowerSpectrum/PowerSpectrum.m b/Protocols/PowerSpectrum/PowerSpectrum.m
new file mode 100644
index 0000000..faa17bd
--- /dev/null
+++ b/Protocols/PowerSpectrum/PowerSpectrum.m
@@ -0,0 +1,136 @@
+% Creates a single stimulus composed of mean + flash for Red,Green,Blue LEDs
+% Implements SymphonyProtocol
+%
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+%
+%  Modified by TA 17.9.12 from LED Family to create a single LED pulse
+%  protocol but also plots the power spectrum of the input
+classdef PowerSpectrum < SymphonyProtocol
+
+    properties (Constant)
+        identifier = 'helsinki.yliopisto.pal'
+        version = 1
+        displayName = 'Power Spectrum'
+    end
+    
+    properties
+        stimPoints = uint16(100);
+        prePoints = uint16(1000);
+        tailPoints = uint16(4000);
+        stimAmplitude = 0.5;
+        lightMean = 0.0;
+        preSynapticHold = -60;
+        numberOfAverages = uint8(5);
+        interpulseInterval = 0.6;
+        continuousRun = false;
+        LED = {'Red_LED','Green_LED','Blue_LED'};
+    end
+    
+    properties (Dependent = true, SetAccess = private) % these properties are inherited - i.e., not modifiable
+        % ampOfLastStep;
+    end
+    
+    methods
+        
+        function [stimulus, lightAmplitude] = stimulusForEpoch(obj, ~) % epoch Num is usually required
+            % Calculate the light amplitude for this epoch.
+            % phase = single(mod(epochNum - 1, obj.stepsInFamily));               % Frank's clever way to determine which flash in a family to deliver
+            lightAmplitude = obj.stimAmplitude; % * obj.ampStepScale ^ phase;   % Frank's clever way to determine the amplitude of the flash family to deliver
+            
+            % Create the stimulus
+            stimulus = ones(1, obj.prePoints + obj.stimPoints + obj.tailPoints) * obj.lightMean;
+            stimulus(obj.prePoints + 1:obj.prePoints + obj.stimPoints) = lightAmplitude;
+        end
+        
+        
+        function stimulus = sampleStimuli(obj) % Return a cell array
+            % you can only create one stimulus with this protocol TA
+            stimulus{1} = obj.stimulusForEpoch();
+        end
+        
+        
+        function prepareRig(obj)
+            % Call the base class method to set the DAQ sample rate.
+            prepareRig@SymphonyProtocol(obj);
+            
+            %obj.setDeviceBackground('LED', obj.lightMean, 'V');
+            
+%             if strcmp(obj.rigConfig.multiClampMode('Amplifier_Ch1'), 'IClamp')
+%                 obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-12, 'A');
+%             else
+%                 obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-3, 'V');
+%             end
+        end
+        
+        
+        function prepareRun(obj)
+            % Call the base class method which clears all figures.
+            prepareRun@SymphonyProtocol(obj);
+
+            obj.openFigure('Response');
+            obj.openFigure('Power Spectrum','GroupByParams', {'lightAmplitude'});
+            % obj.openFigure('Mean PS', 'GroupByParams', {'lightAmplitude'});
+            % obj.openFigure('PS Response Statistics', 'StatsCallback', @responseStatistics);
+        end
+        
+        
+        function prepareEpoch(obj)
+            % Call the base class method which sets up default backgrounds and records responses.
+            prepareEpoch@SymphonyProtocol(obj);
+            
+            [stimulus, lightAmplitude] = obj.stimulusForEpoch(obj.epochNum);
+            obj.addParameter('lightAmplitude', lightAmplitude);
+            %obj.addStimulus('LED', 'test-stimulus', stimulus, 'V');    %
+            obj.setDeviceBackground(obj.LED, obj.lightMean, 'V');
+            if strcmp(obj.multiClampMode, 'VClamp')
+                obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-3, 'V');
+            else
+                obj.setDeviceBackground('Amplifier_Ch1', double(obj.preSynapticHold) * 1e-12, 'A');
+            end 
+            obj.addStimulus(obj.LED, sprintf('%s stimulus',obj.LED), stimulus, 'V');    %
+        end
+        
+        
+        function stats = responseStatistics(obj)
+            r = obj.response();
+            
+            % baseline mean and var
+            if ~isempty(r)
+                stats.mean = mean(r(1:obj.prePoints));
+                stats.var = var(r(1:obj.prePoints));
+            else
+                stats.mean = 0;
+                stats.var = 0;
+            end
+        end
+        
+        
+        function completeEpoch(obj)
+            % Call the base class method which updates the figures.
+            completeEpoch@SymphonyProtocol(obj);
+            
+            % Pause for the inter-pulse interval.
+            pause on
+            pause(obj.interpulseInterval);
+        end
+        
+        
+        function keepGoing = continueRun(obj)   
+            % First check the base class method to make sure the user hasn't paused or stopped the protocol.
+            keepGoing = continueRun@SymphonyProtocol(obj);
+            
+            if keepGoing
+                keepGoing = obj.epochNum < obj.numberOfAverages;
+            end
+        end
+        
+        
+%         function amp = get.ampOfLastStep(obj)   % The product of the number of steps in family, the first step amplitude, and the 'scale factor'
+%             amp = obj.baseLightAmplitude * obj.ampStepScale ^ (obj.stepsInFamily - 1);
+%         end
+
+    end
+end
\ No newline at end of file
diff --git a/Protocols/RFcircleMapping/allcombs.m b/Protocols/RFcircleMapping/allcombs.m
deleted file mode 100644
index 71ef394..0000000
--- a/Protocols/RFcircleMapping/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/RFgridMapping/allcombs.m b/Protocols/RFgridMapping/allcombs.m
deleted file mode 100644
index 71ef394..0000000
--- a/Protocols/RFgridMapping/allcombs.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/Circle/Circle.m b/Protocols_extra/Circle/Circle.m
similarity index 100%
rename from Protocols/Circle/Circle.m
rename to Protocols_extra/Circle/Circle.m
diff --git a/Protocols/Circle/allcombs.m b/Protocols_extra/Circle/allcombs.m
similarity index 96%
rename from Protocols/Circle/allcombs.m
rename to Protocols_extra/Circle/allcombs.m
index 71ef394..6bbe699 100644
--- a/Protocols/Circle/allcombs.m
+++ b/Protocols_extra/Circle/allcombs.m
@@ -1,37 +1,37 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/DS_V1/DS_V1.m b/Protocols_extra/DS_V1/DS_V1.m
similarity index 100%
rename from Protocols/DS_V1/DS_V1.m
rename to Protocols_extra/DS_V1/DS_V1.m
diff --git a/Protocols/DS_V1/allcombs.m b/Protocols_extra/DS_V1/allcombs.m
similarity index 96%
rename from Protocols/DS_V1/allcombs.m
rename to Protocols_extra/DS_V1/allcombs.m
index 71ef394..6bbe699 100644
--- a/Protocols/DS_V1/allcombs.m
+++ b/Protocols_extra/DS_V1/allcombs.m
@@ -1,37 +1,37 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/DS_V2/DS_V2.m b/Protocols_extra/DS_V2/DS_V2.m
similarity index 100%
rename from Protocols/DS_V2/DS_V2.m
rename to Protocols_extra/DS_V2/DS_V2.m
diff --git a/Protocols/DS_V2/allcombs.m b/Protocols_extra/DS_V2/allcombs.m
similarity index 96%
rename from Protocols/DS_V2/allcombs.m
rename to Protocols_extra/DS_V2/allcombs.m
index 71ef394..6bbe699 100644
--- a/Protocols/DS_V2/allcombs.m
+++ b/Protocols_extra/DS_V2/allcombs.m
@@ -1,37 +1,37 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/ExpandingObjects/ExpandingObjects.m b/Protocols_extra/ExpandingObjects/ExpandingObjects.m
similarity index 100%
rename from Protocols/ExpandingObjects/ExpandingObjects.m
rename to Protocols_extra/ExpandingObjects/ExpandingObjects.m
diff --git a/Protocols/ExpandingObjects/allcombs.m b/Protocols_extra/ExpandingObjects/allcombs.m
similarity index 96%
rename from Protocols/ExpandingObjects/allcombs.m
rename to Protocols_extra/ExpandingObjects/allcombs.m
index 71ef394..6bbe699 100644
--- a/Protocols/ExpandingObjects/allcombs.m
+++ b/Protocols_extra/ExpandingObjects/allcombs.m
@@ -1,37 +1,37 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function A = allcombs(varargin)
-
-% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
-% modified so it can take a scalar (or vector) as the first input
-
-% modified part1
-if numel(varargin{1})==1
-    varargin{1} = [varargin{1} NaN];
-end
-    
-% simplified version of allcomb function
-q = ~cellfun('isempty',varargin);
-ni = sum(q) ;
-ii = ni:-1:1 ;
-if ni==0,
-    A = [] ;
-else
-    args = varargin(q) ;
-
-    if ni==1,
-        A = args{1}(:) ;
-    else
-        % flip using ii if last column is changing fastest
-        [A{ii}] = ndgrid(args{ii}) ;
-        % concatenate
-        A = reshape(cat(ni+1,A{:}),[],ni) ;
-    end
-end
-% end of allcomb function
-
-% modified part2
-A(isnan(A(:,1)),:) = [];
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/Grid/Grid.m b/Protocols_extra/Grid/Grid.m
similarity index 100%
rename from Protocols/Grid/Grid.m
rename to Protocols_extra/Grid/Grid.m
diff --git a/Protocols_extra/Grid/allcombs.m b/Protocols_extra/Grid/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/Grid/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/Grid/calcEllipse.m b/Protocols_extra/Grid/calcEllipse.m
similarity index 98%
rename from Protocols/Grid/calcEllipse.m
rename to Protocols_extra/Grid/calcEllipse.m
index e424251..a971c94 100644
--- a/Protocols/Grid/calcEllipse.m
+++ b/Protocols_extra/Grid/calcEllipse.m
@@ -1,9 +1,9 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function [X Y] = calcEllipse(x,y,a,b,angle)
-% calculate points for plotting ellipse
-X=x+(a*cosd(0:360)*cosd(angle)-b*sind(0:360)*sind(angle));
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function [X Y] = calcEllipse(x,y,a,b,angle)
+% calculate points for plotting ellipse
+X=x+(a*cosd(0:360)*cosd(angle)-b*sind(0:360)*sind(angle));
 Y=y+(a*cosd(0:360)*sind(angle)+b*sind(0:360)*cosd(angle));
\ No newline at end of file
diff --git a/Protocols/Grid/gauss2Dfit.m b/Protocols_extra/Grid/gauss2Dfit.m
similarity index 98%
rename from Protocols/Grid/gauss2Dfit.m
rename to Protocols_extra/Grid/gauss2Dfit.m
index 94bbeca..32f910a 100644
--- a/Protocols/Grid/gauss2Dfit.m
+++ b/Protocols_extra/Grid/gauss2Dfit.m
@@ -1,44 +1,44 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-function [RFstring muX muY sigmaX sigmaY rotationAngle]=gauss2Dfit(Xcoords,Ycoords,meanResp)
-x=Xcoords(1):-1:Xcoords(end);
-y=Ycoords(1):Ycoords(end);
-meanRespIntp=interp2(Xcoords,Ycoords,meanResp,x,y','linear');
-errorFunc=@(p) sum((meanRespIntp(:)-gauss2D(p,x,y)).^2);
-peakResp=max(meanRespIntp(:));
-[peakYindex peakXindex]=find(meanRespIntp==peakResp);
-peakX=x(round(mean(peakXindex)));
-peakY=y(round(mean(peakYindex)));
-halfPeakDiff=abs(meanRespIntp-0.6*peakResp);
-[halfPeakDistYindex halfPeakDistXindex]=find(halfPeakDiff==min(halfPeakDiff(:)));
-halfPeakDistX=abs(peakX-x(round(mean(halfPeakDistXindex))));
-halfPeakDistY=abs(peakY-y(round(mean(halfPeakDistYindex))));
-seedValues=[peakResp*2*pi*halfPeakDistX*halfPeakDistY,peakX,peakY,halfPeakDistX,halfPeakDistY,0];
-fitParams=fminsearch(errorFunc,seedValues,optimset('MaxFunEvals',1e5,'MaxIter',1e5));
-fitR=corrcoef(meanResp,gauss2D(fitParams,Xcoords,Ycoords));
-fitRsq=round((fitR(1,2)^2)*100)/100;
-roundFitParams=round(fitParams*10)/10;
-RFstring=['RF: center [' num2str(roundFitParams(2)) ',' num2str(roundFitParams(3)) '], sd [' num2str(roundFitParams(4)) ',' num2str(roundFitParams(5)) '], rotation ' num2str(roundFitParams(6)) ' deg, fit r sq = ' num2str(fitRsq)];
-rotationAngle=roundFitParams(6);
-% convert mu and sigma from degrees to image pixel coordinates
-pixPerDeg=(numel(Ycoords)-1)/(Ycoords(end)-Ycoords(1));
-muX=pixPerDeg*(x(1)-fitParams(2))+1;
-muY=pixPerDeg*(y(end)-fitParams(3))+1;
-sigmaX=fitParams(4)*pixPerDeg;
-sigmaY=fitParams(5)*pixPerDeg;
-
-
-function z=gauss2D(p,x,y)
-coords=allcombs(x,y);
-% p(1:6)=[V,muX,muY,sigmaX,sigmaY,theta]
-% 2D gauss with rotation, http://en.wikipedia.org/wiki/Gaussian_function
-z = (p(1)/(2*pi*p(4)*p(5)))*exp(-(...
-    ((cosd(p(6))^2)/(2*p(4)^2)+(sind(p(6))^2)/(2*p(5)^2))*((coords(:,1)-p(2)).^2) +...
-    2*((sind(2*p(6)))/(4*p(4)^2)+(sind(2*p(6)))/(4*p(5)^2))*(coords(:,1)-p(2)).*(coords(:,2)-p(3)) +...
-    ((sind(p(6))^2)/(2*p(4)^2)+(cosd(p(6))^2)/(2*p(5)^2))*((coords(:,2)-p(3)).^2)...
-    ));
-% 2D gauss without rotation
-% z=(p(1)/(2*pi*p(4)*p(5)))*exp(-((((coords(:,1)-p(2)).^2)/(2*p(4)^2))+(((coords(:,2)-p(3)).^2)/(2*p(5)^2))));
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function [RFstring muX muY sigmaX sigmaY rotationAngle]=gauss2Dfit(Xcoords,Ycoords,meanResp)
+x=Xcoords(1):-1:Xcoords(end);
+y=Ycoords(1):Ycoords(end);
+meanRespIntp=interp2(Xcoords,Ycoords,meanResp,x,y','linear');
+errorFunc=@(p) sum((meanRespIntp(:)-gauss2D(p,x,y)).^2);
+peakResp=max(meanRespIntp(:));
+[peakYindex peakXindex]=find(meanRespIntp==peakResp);
+peakX=x(round(mean(peakXindex)));
+peakY=y(round(mean(peakYindex)));
+halfPeakDiff=abs(meanRespIntp-0.6*peakResp);
+[halfPeakDistYindex halfPeakDistXindex]=find(halfPeakDiff==min(halfPeakDiff(:)));
+halfPeakDistX=abs(peakX-x(round(mean(halfPeakDistXindex))));
+halfPeakDistY=abs(peakY-y(round(mean(halfPeakDistYindex))));
+seedValues=[peakResp*2*pi*halfPeakDistX*halfPeakDistY,peakX,peakY,halfPeakDistX,halfPeakDistY,0];
+fitParams=fminsearch(errorFunc,seedValues,optimset('MaxFunEvals',1e5,'MaxIter',1e5));
+fitR=corrcoef(meanResp,gauss2D(fitParams,Xcoords,Ycoords));
+fitRsq=round((fitR(1,2)^2)*100)/100;
+roundFitParams=round(fitParams*10)/10;
+RFstring=['RF: center [' num2str(roundFitParams(2)) ',' num2str(roundFitParams(3)) '], sd [' num2str(roundFitParams(4)) ',' num2str(roundFitParams(5)) '], rotation ' num2str(roundFitParams(6)) ' deg, fit r sq = ' num2str(fitRsq)];
+rotationAngle=roundFitParams(6);
+% convert mu and sigma from degrees to image pixel coordinates
+pixPerDeg=(numel(Ycoords)-1)/(Ycoords(end)-Ycoords(1));
+muX=pixPerDeg*(x(1)-fitParams(2))+1;
+muY=pixPerDeg*(y(end)-fitParams(3))+1;
+sigmaX=fitParams(4)*pixPerDeg;
+sigmaY=fitParams(5)*pixPerDeg;
+
+
+function z=gauss2D(p,x,y)
+coords=allcombs(x,y);
+% p(1:6)=[V,muX,muY,sigmaX,sigmaY,theta]
+% 2D gauss with rotation, http://en.wikipedia.org/wiki/Gaussian_function
+z = (p(1)/(2*pi*p(4)*p(5)))*exp(-(...
+    ((cosd(p(6))^2)/(2*p(4)^2)+(sind(p(6))^2)/(2*p(5)^2))*((coords(:,1)-p(2)).^2) +...
+    2*((sind(2*p(6)))/(4*p(4)^2)+(sind(2*p(6)))/(4*p(5)^2))*(coords(:,1)-p(2)).*(coords(:,2)-p(3)) +...
+    ((sind(p(6))^2)/(2*p(4)^2)+(cosd(p(6))^2)/(2*p(5)^2))*((coords(:,2)-p(3)).^2)...
+    ));
+% 2D gauss without rotation
+% z=(p(1)/(2*pi*p(4)*p(5)))*exp(-((((coords(:,1)-p(2)).^2)/(2*p(4)^2))+(((coords(:,2)-p(3)).^2)/(2*p(5)^2))));
diff --git a/Protocols/HotspotsDS/HotspotsDS.m b/Protocols_extra/HotspotsDS/HotspotsDS.m
old mode 100755
new mode 100644
similarity index 100%
rename from Protocols/HotspotsDS/HotspotsDS.m
rename to Protocols_extra/HotspotsDS/HotspotsDS.m
diff --git a/Protocols_extra/HotspotsDS/allcombs.m b/Protocols_extra/HotspotsDS/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/HotspotsDS/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/LEDpulse/LEDpulse.m b/Protocols_extra/LEDpulse/LEDpulse.m
similarity index 100%
rename from Protocols/LEDpulse/LEDpulse.m
rename to Protocols_extra/LEDpulse/LEDpulse.m
diff --git a/Protocols/LoomingObjects/LoomingObjects.m b/Protocols_extra/LoomingObjects/LoomingObjects.m
similarity index 100%
rename from Protocols/LoomingObjects/LoomingObjects.m
rename to Protocols_extra/LoomingObjects/LoomingObjects.m
diff --git a/Protocols_extra/LoomingObjects/allcombs.m b/Protocols_extra/LoomingObjects/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/LoomingObjects/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/MovingBar/MovingBar.m b/Protocols_extra/MovingBar/MovingBar.m
similarity index 100%
rename from Protocols/MovingBar/MovingBar.m
rename to Protocols_extra/MovingBar/MovingBar.m
diff --git a/Protocols_extra/MovingBar/allcombs.m b/Protocols_extra/MovingBar/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/MovingBar/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/MovingGrid/MovingGrid.m b/Protocols_extra/MovingGrid/MovingGrid.m
similarity index 100%
rename from Protocols/MovingGrid/MovingGrid.m
rename to Protocols_extra/MovingGrid/MovingGrid.m
diff --git a/Protocols_extra/MovingGrid/allcombs.m b/Protocols_extra/MovingGrid/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/MovingGrid/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/MovingObjects/MovingObjects.m b/Protocols_extra/MovingObjects/MovingObjects.m
similarity index 100%
rename from Protocols/MovingObjects/MovingObjects.m
rename to Protocols_extra/MovingObjects/MovingObjects.m
diff --git a/Protocols_extra/MovingObjects/allcombs.m b/Protocols_extra/MovingObjects/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/MovingObjects/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/MovingObjectsProtocol/MovingObjectsProtocol.m b/Protocols_extra/MovingObjectsProtocol/MovingObjectsProtocol.m
similarity index 100%
rename from Protocols/MovingObjectsProtocol/MovingObjectsProtocol.m
rename to Protocols_extra/MovingObjectsProtocol/MovingObjectsProtocol.m
diff --git a/Protocols/RFcircleMapping/RFcircleMapping.m b/Protocols_extra/RFcircleMapping/RFcircleMapping.m
similarity index 100%
rename from Protocols/RFcircleMapping/RFcircleMapping.m
rename to Protocols_extra/RFcircleMapping/RFcircleMapping.m
diff --git a/Protocols_extra/RFcircleMapping/allcombs.m b/Protocols_extra/RFcircleMapping/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/RFcircleMapping/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/RFgridMapping/RFgridMapping.m b/Protocols_extra/RFgridMapping/RFgridMapping.m
similarity index 100%
rename from Protocols/RFgridMapping/RFgridMapping.m
rename to Protocols_extra/RFgridMapping/RFgridMapping.m
diff --git a/Protocols_extra/RFgridMapping/allcombs.m b/Protocols_extra/RFgridMapping/allcombs.m
new file mode 100644
index 0000000..6bbe699
--- /dev/null
+++ b/Protocols_extra/RFgridMapping/allcombs.m
@@ -0,0 +1,37 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+function A = allcombs(varargin)
+
+% simplified version of Jos van der Geest's allcomb.m function from the matlab file exchange
+% modified so it can take a scalar (or vector) as the first input
+
+% modified part1
+if numel(varargin{1})==1
+    varargin{1} = [varargin{1} NaN];
+end
+    
+% simplified version of allcomb function
+q = ~cellfun('isempty',varargin);
+ni = sum(q) ;
+ii = ni:-1:1 ;
+if ni==0,
+    A = [] ;
+else
+    args = varargin(q) ;
+
+    if ni==1,
+        A = args{1}(:) ;
+    else
+        % flip using ii if last column is changing fastest
+        [A{ii}] = ndgrid(args{ii}) ;
+        % concatenate
+        A = reshape(cat(ni+1,A{:}),[],ni) ;
+    end
+end
+% end of allcomb function
+
+% modified part2
+A(isnan(A(:,1)),:) = [];
diff --git a/Protocols/TempInt/TempInt.m b/Protocols_extra/TempInt/TempInt.m
similarity index 100%
rename from Protocols/TempInt/TempInt.m
rename to Protocols_extra/TempInt/TempInt.m
diff --git a/ReadMe.txt b/ReadMe.txt
index ae7e1af..63392bc 100644
--- a/ReadMe.txt
+++ b/ReadMe.txt
@@ -1,5 +1,5 @@
 See Overview.txt in the Documentation folder to get started with Symphony.
-
+Hello Matthew
 ****************************************************************************
 
 The Janelia Farm Research Campus Software Copyright 1.1
diff --git a/Rig Configurations/PALPatchRig.m b/Rig Configurations/PALPatchRig.m
new file mode 100644
index 0000000..9fbcfe6
--- /dev/null
+++ b/Rig Configurations/PALPatchRig.m	
@@ -0,0 +1,25 @@
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+%
+% Modified 27-Aug-2012 TWA to create new Color Rig
+
+classdef PALPatchRig < RigConfiguration
+    
+    properties (Constant)
+        displayName = 'Retina Electrophysiology'
+    end
+    
+    
+    methods
+        
+        function createDevices(obj)
+            obj.addMultiClampDevice('Amplifier_Ch1', 1, 'ANALOG_OUT.0', 'ANALOG_IN.0');
+            obj.addDevice('Red_LED', 'ANALOG_OUT.1', '');   % output only
+            obj.addDevice('Green_LED', 'ANALOG_OUT.2', '');   % output only
+            obj.addDevice('Blue_LED', 'ANALOG_OUT.3', '');   % output only
+        end
+        
+    end
+end
\ No newline at end of file
diff --git a/RigConfiguration.m b/RigConfiguration.m
index 07dd46c..8a1489b 100644
--- a/RigConfiguration.m
+++ b/RigConfiguration.m
@@ -86,7 +86,7 @@
                     elseif strcmp(answer, 'PCI')
                         hekaID = 1;
                     else    % USB
-                        hekaID = 5;
+                        hekaID = double(NativeInterop.ITCMM.USB18_ID);
                     end
                     setpref('Symphony', 'HekaBusID', hekaID);
                 end
diff --git a/StartSymphony.m b/StartSymphony.m
index 8cca717..90277e3 100644
--- a/StartSymphony.m
+++ b/StartSymphony.m
@@ -1,31 +1,49 @@
-%  Copyright (c) 2012 Howard Hughes Medical Institute.
-%  All rights reserved.
-%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
-%  http://license.janelia.org/license/jfrc_copyright_1_1.html
-
-% Wrapper script (NOT a function) to load the Symphony .NET assemblies correctly.
-
-if verLessThan('matlab', '7.12')
-    error('Symphony requires MATLAB 7.12.0 (R2011a) or later');
-end
-
-% Add our utility and figure handler folders to the search path.
-symphonyPath = mfilename('fullpath');
-parentDir = fileparts(symphonyPath);
-addpath(fullfile(parentDir, 'Utility'));
-addpath(fullfile(parentDir, 'Rig Configurations'));
-addpath(fullfile(parentDir, 'Figure Handlers'));
-addpath(fullfile(parentDir, 'StimGL'));
-clear symphonyPath parentDir
-
-% Load the Symphony .NET framework
-addSymphonyFramework();
-
-% Launch the user interface
-global symphonyInstance;
-
-if isempty(symphonyInstance)
-    symphonyInstance = Symphony();
-else
-    symphonyInstance.showMainWindow();
-end
+%  Copyright (c) 2012 Howard Hughes Medical Institute.
+%  All rights reserved.
+%  Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
+%  http://license.janelia.org/license/jfrc_copyright_1_1.html
+
+% Wrapper script (NOT a function) to load the Symphony .NET assemblies correctly.
+
+if verLessThan('matlab', '7.12')
+    error('Symphony requires MATLAB 7.12.0 (R2011a) or later');
+end
+
+% Add our utility and figure handler folders to the search path.
+symphonyPath = mfilename('fullpath');
+parentDir = fileparts(symphonyPath);
+addpath(fullfile(parentDir, 'Utility'));
+addpath(fullfile(parentDir, 'Rig Configurations'));
+addpath(fullfile(parentDir, 'Figure Handlers'));
+addpath(fullfile(parentDir, 'StimGL'));
+clear symphonyPath parentDir
+
+% Load the Symphony .NET framework
+%addSymphonyFramework();
+
+if isempty(which('NET.convertArray'))
+    % Use the .NET stub classes instead of the real thing on non-PC platforms.
+    symphonyPath = mfilename('fullpath');
+    parentDir = fileparts(symphonyPath);
+    addpath(fullfile(parentDir, filesep, 'Stubs'));
+else
+    symphonyPath = 'C:\Program Files\Physion\Symphony\bin';
+    
+    % Add Symphony.Core assemblies
+    NET.addAssembly(fullfile(symphonyPath, 'Symphony.Core.dll'));
+    NET.addAssembly(fullfile(symphonyPath, 'Symphony.ExternalDevices.dll'));
+    NET.addAssembly(fullfile(symphonyPath, 'HekaDAQInterface.dll'));
+    NET.addAssembly(fullfile(symphonyPath, 'Symphony.SimulationDAQController.dll'));
+    
+    NET.addAssembly('System.Windows.Forms');
+end
+
+
+% Launch the user interface
+global symphonyInstance;
+
+if isempty(symphonyInstance)
+    symphonyInstance = Symphony();
+else
+    symphonyInstance.showMainWindow();
+end
diff --git a/Symphony.m b/Symphony.m
index 179996f..67f6505 100644
--- a/Symphony.m
+++ b/Symphony.m
@@ -998,7 +998,7 @@ function createNewEpochGroup(obj, ~, ~)
                     
                     obj.metadataDoc = com.mathworks.xml.XMLUtils.createDocument('symphony-metadata');
                     obj.metadataNode = obj.metadataDoc.getDocumentElement();
-                    
+
                     if exist(obj.persistPath, 'file')
                         % Make sure we have the same source UUID's as before.
                         [pathstr, name, ~] = fileparts(obj.persistPath);
@@ -1032,9 +1032,12 @@ function createNewEpochGroup(obj, ~, ~)
                     
                     if ismac
                         obj.persistor = EpochXMLPersistor(obj.persistPath);
-                    else
-                        obj.persistor = EpochHDF5Persistor(obj.persistPath, '', 9);
+                    else 
+                        obj.persistor = EpochHDF5Persistor(obj.persistPath,System.String(''), 9);
                     end
+                    
+                    obj.saveMetadata();
+
                 end
                 
                 obj.epochGroup = group;
@@ -1064,8 +1067,11 @@ function closeEpochGroup(obj, ~, ~)
                 else
                     obj.epochGroup = obj.epochGroup.parentGroup;
                 end
+                %obj.saveMetadata();
+
             else
                 obj.persistor.CloseDocument();
+                obj.persistor.Dispose();
                 obj.persistor = [];
                 
                 % Break the reference loop on the group hierarchy so they all get deleted.